Reading info.rhd file...

Reading Intan Technologies RHD2000 Data File, Version 1.5

n signal groups 7
Found 32 amplifier channels.
Found 3 auxiliary input channels.
Found 1 supply voltage channel.
Found 0 board ADC channels.
Found 1 board digital input channel.
Found 0 board digital output channels.
Found 0 temperature sensors channels.

Header file contains no data.  Amplifiers were sampled at 30.00 kS/s.
Done!  Elapsed time: 0.0 seconds

Recording Info
--------------

amplifier_sampling_rate    30000.0
dig_in_sampling_rate       30000.0
notch_filter               60
ports                      
    C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C, C
channels                   
    0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31
num_channels               32
dig_in                     
    0
file_type                  one file per channel

clustering_params.json not found in recording directory. Pulling parameters from defaults
spike_array_params.json not found in recording directory. Pulling parameters from defaults
psth_params.json not found in recording directory. Pulling parameters from defaults
pal_id_params.json not found in recording directory. Pulling parameters from defaults
CAR_params.json not found in recording directory. Pulling parameters from defaults
Writing parameters to JSON...Writing all parameters to json file in analysis_params folder...

Saved RN27_ctaTrain to /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain_dataset.p


Extract Intan Data
--------------------
Creating empty HDF5 store with raw data groups
Writing RN27_ctaTrain.h5 ...Done!

Creating empty arrays in hdf5 store for raw data...Done!
Extracting Intan data to HDF5 Store:
 h5 file: /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain.h5

Reading time data...
Writing time data...Done!

----------
Extracting Digital Signal Data
----------
Reading digitalin data from board-DIN-00.dat...Done!
Writing data from ditigal in channel 0 to dig_in_0...Done!
Done! Elapsed Time: 0.73


----------
Extracting Amplifier Signal Data
----------
Reading data from amp-C-000.dat...Done!
Writing data from port C channel 0 to electrode0...Done!
Reading data from amp-C-001.dat...Done!
Writing data from port C channel 1 to electrode1...Done!
Reading data from amp-C-002.dat...Done!
Writing data from port C channel 2 to electrode2...Done!
Reading data from amp-C-003.dat...Done!
Writing data from port C channel 3 to electrode3...Done!
Reading data from amp-C-004.dat...Done!
Writing data from port C channel 4 to electrode4...Done!
Reading data from amp-C-005.dat...Done!
Writing data from port C channel 5 to electrode5...Done!
Reading data from amp-C-006.dat...Done!
Writing data from port C channel 6 to electrode6...Done!
Reading data from amp-C-007.dat...Done!
Writing data from port C channel 7 to electrode7...Done!
Reading data from amp-C-008.dat...Done!
Writing data from port C channel 8 to electrode8...Done!
Reading data from amp-C-009.dat...Done!
Writing data from port C channel 9 to electrode9...Done!
Reading data from amp-C-010.dat...Done!
Writing data from port C channel 10 to electrode10...Done!
Reading data from amp-C-011.dat...Done!
Writing data from port C channel 11 to electrode11...Done!
Reading data from amp-C-012.dat...Done!
Writing data from port C channel 12 to electrode12...Done!
Reading data from amp-C-013.dat...Done!
Writing data from port C channel 13 to electrode13...Done!
Reading data from amp-C-014.dat...Done!
Writing data from port C channel 14 to electrode14...Done!
Reading data from amp-C-015.dat...Done!
Writing data from port C channel 15 to electrode15...Done!
Reading data from amp-C-016.dat...Done!
Writing data from port C channel 16 to electrode16...Done!
Reading data from amp-C-017.dat...Done!
Writing data from port C channel 17 to electrode17...Done!
Reading data from amp-C-018.dat...Done!
Writing data from port C channel 18 to electrode18...Done!
Reading data from amp-C-019.dat...Done!
Writing data from port C channel 19 to electrode19...Done!
Reading data from amp-C-020.dat...Done!
Writing data from port C channel 20 to electrode20...Done!
Reading data from amp-C-021.dat...Done!
Writing data from port C channel 21 to electrode21...Done!
Reading data from amp-C-022.dat...Done!
Writing data from port C channel 22 to electrode22...Done!
Reading data from amp-C-023.dat...Done!
Writing data from port C channel 23 to electrode23...Done!
Reading data from amp-C-024.dat...Done!
Writing data from port C channel 24 to electrode24...Done!
Reading data from amp-C-025.dat...Done!
Writing data from port C channel 25 to electrode25...Done!
Reading data from amp-C-026.dat...Done!
Writing data from port C channel 26 to electrode26...Done!
Reading data from amp-C-027.dat...Done!
Writing data from port C channel 27 to electrode27...Done!
Reading data from amp-C-028.dat...Done!
Writing data from port C channel 28 to electrode28...Done!
Reading data from amp-C-029.dat...Done!
Writing data from port C channel 29 to electrode29...Done!
Reading data from amp-C-030.dat...Done!
Writing data from port C channel 30 to electrode30...Done!
Reading data from amp-C-031.dat...Done!
Writing data from port C channel 31 to electrode31...Done!
Done! Elapsed Time: 30.33

Writing electrode_map to /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain.h5...
Writing digital_input_map to /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain.h5...
Saved RN27_ctaTrain to /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain_dataset.p


Data Extraction Complete
--------------------

----------
Gathering Trial Data and Creating Table
----------
Generating trial list for digital inputs: 0
Constructing DataFrame...Done!
Writing data to h5 file...Done!
Done! Elapsed Time: 0.28

No digital output data found
Saved RN27_ctaTrain to /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain_dataset.p

Marking dead channels
----------
Marking eletrodes [8, 9] as dead.
They will be excluded from common average referencing.
Writing electrode_map to /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain.h5...
Saved RN27_ctaTrain to /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain_dataset.p

CAR Groups

Group 0	Group 1
-------	-------
0	8
1	9
2	10
3	11
4	12
5	13
6	14
7	15
24	16
25	17
26	18
27	19
28	20
29	21
30	22
31	23

----------
Common Average Referencing
----------
Common Average Referencing Electrodes:
0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27, 28, 29, 30, 31
Computing common average...Done!
Storing common average signal...Done!
Storing referenced signals...Done!
Done! Elapsed Time: 33.18


----------
Common Average Referencing
----------
Common Average Referencing Electrodes:
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
Computing common average...Done!
Storing common average signal...Done!
Storing referenced signals...Done!
Done! Elapsed Time: 30.92


----------
Compressing and repacking h5 file
----------
Repacking /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain.h5 as /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/tmp.h5...
Removing old h5 file: /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain.h5
Renaming temporary file to /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain.h5
Done! Elapsed Time: 101.19

Saved RN27_ctaTrain to /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain_dataset.p


Running Spike Detection
-------------------
Parameters
file_dir             /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440
data_quality         clean
sampling_rate        30000.0
clustering_params    
    Max Number of Clusters      7
    Max Number of Iterations    1000
    Convergence Criterion       0.001
    GMM random restarts         10
    
data_params          
    V_cutoff for disconnected headstage     1500
    Max rate of cutoff breach per second    0.2
    Max allowed seconds with a breach       10
    Max allowed breaches per second         20
    Intra-cluster waveform amp SD cutoff    3
    
bandpass_params      
    Lower freq cutoff    300
    Upper freq cutoff    3000
    
spike_snapshot       
    Time before spike (ms)    0.5
    Time after spike (ms)     1
    

Electrode    Result    Cutoff (s)
  0            1         1466
  1            1         1466
  2            1         1466
  3            1         1466
  4            1         1466
  5            1         1466
  6            1         1466
  7            1         1466
  10           1         1466
  11           1         1466
  12           1         1466
  13           1         1466
  14           1         1466
  15           1         1466
  16           1         1466
  17           1         1466
  18           1         1466
  19           1         1466
  20           1         1466
  21           1         1466
  22           1         1466
  23           1         1466
  24           1         1466
  25           1         1466
  26           1         1466
  27           1         1466
  28           1         1466
  29           1         1466
  30           1         1466
  31           1         1466
1 - Sucess
0 - No data or no spikes
-1 - Error
Writing electrode_map to /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain.h5...
Saved RN27_ctaTrain to /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain_dataset.p

Spike Detection Complete
------------------

Running Blech Clust
-------------------
Parameters
file_dir             /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440
data_quality         clean
sampling_rate        30000.0
clustering_params    
    Max Number of Clusters      15
    Max Number of Iterations    1000
    Convergence Criterion       0.001
    GMM random restarts         10
    
data_params          
    V_cutoff for disconnected headstage     1500
    Max rate of cutoff breach per second    0.2
    Max allowed seconds with a breach       10
    Max allowed breaches per second         20
    Intra-cluster waveform amp SD cutoff    3
    
bandpass_params      
    Lower freq cutoff    300
    Upper freq cutoff    3000
    
spike_snapshot       
    Time before spike (ms)    0.5
    Time after spike (ms)     1
    

Writing electrode_map to /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain.h5...
Saved RN27_ctaTrain to /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain_dataset.p

Clustering Complete
------------------

----------
Clustering Cleanup
----------
Removing raw data from hdf5 store...Done!
Removing referenced data from hdf5 store...Done!

----------
Compressing and repacking h5 file
----------
Repacking /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain.h5 as /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/tmp.h5...
Removing old h5 file: /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain.h5
Renaming temporary file to /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain.h5
Done! Elapsed Time: 9.24

Done! Elapsed Time: 14.34

Saved RN27_ctaTrain to /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain_dataset.p


---------
Beginning unit similarity calculation
----------
Computing similarity between Unit 0 and Unit 0
Computing similarity between Unit 0 and Unit 1
Computing similarity between Unit 0 and Unit 2
Computing similarity between Unit 0 and Unit 3
Computing similarity between Unit 0 and Unit 4
Computing similarity between Unit 0 and Unit 5
Computing similarity between Unit 0 and Unit 6
Computing similarity between Unit 0 and Unit 7
Computing similarity between Unit 1 and Unit 0
Computing similarity between Unit 1 and Unit 1
Computing similarity between Unit 1 and Unit 2
Computing similarity between Unit 1 and Unit 3
Computing similarity between Unit 1 and Unit 4
Computing similarity between Unit 1 and Unit 5
Computing similarity between Unit 1 and Unit 6
Computing similarity between Unit 1 and Unit 7
Computing similarity between Unit 2 and Unit 0
Computing similarity between Unit 2 and Unit 1
Computing similarity between Unit 2 and Unit 2
Computing similarity between Unit 2 and Unit 3
Computing similarity between Unit 2 and Unit 4
Computing similarity between Unit 2 and Unit 5
Computing similarity between Unit 2 and Unit 6
Computing similarity between Unit 2 and Unit 7
Computing similarity between Unit 3 and Unit 0
Computing similarity between Unit 3 and Unit 1
Computing similarity between Unit 3 and Unit 2
Computing similarity between Unit 3 and Unit 3
Computing similarity between Unit 3 and Unit 4
Computing similarity between Unit 3 and Unit 5
Computing similarity between Unit 3 and Unit 6
Computing similarity between Unit 3 and Unit 7
Computing similarity between Unit 4 and Unit 0
Computing similarity between Unit 4 and Unit 1
Computing similarity between Unit 4 and Unit 2
Computing similarity between Unit 4 and Unit 3
Computing similarity between Unit 4 and Unit 4
Computing similarity between Unit 4 and Unit 5
Computing similarity between Unit 4 and Unit 6
Computing similarity between Unit 4 and Unit 7
Computing similarity between Unit 5 and Unit 0
Computing similarity between Unit 5 and Unit 1
Computing similarity between Unit 5 and Unit 2
Computing similarity between Unit 5 and Unit 3
Computing similarity between Unit 5 and Unit 4
Computing similarity between Unit 5 and Unit 5
Computing similarity between Unit 5 and Unit 6
Computing similarity between Unit 5 and Unit 7
Computing similarity between Unit 6 and Unit 0
Computing similarity between Unit 6 and Unit 1
Computing similarity between Unit 6 and Unit 2
Computing similarity between Unit 6 and Unit 3
Computing similarity between Unit 6 and Unit 4
Computing similarity between Unit 6 and Unit 5
Computing similarity between Unit 6 and Unit 6
Computing similarity between Unit 6 and Unit 7
Computing similarity between Unit 7 and Unit 0
Computing similarity between Unit 7 and Unit 1
Computing similarity between Unit 7 and Unit 2
Computing similarity between Unit 7 and Unit 3
Computing similarity between Unit 7 and Unit 4
Computing similarity between Unit 7 and Unit 5
Computing similarity between Unit 7 and Unit 6
Computing similarity between Unit 7 and Unit 7

Similarity calculation done!
No unit similarity violations found!
Saved RN27_ctaTrain to /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain_dataset.p

Generating unit arrays with parameters:
----------
    dig_ins_to_use    
            0
    laser_channels    
        
    sampling_rate     30000.0
    pre_stimulus      2000
    post_stimulus     5000
    

----------
Making Unit Spike Arrays
----------


----------
Reading Trial Data Table From Store
----------
Done! Elapsed Time: 0.01


----------
Reading Trial Data Table From Store
----------
Done! Elapsed Time: 0.01

Creating spike arrays for dig_in_0...
Done with spike array creation!
----------

Saved RN27_ctaTrain to /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain_dataset.p

Saved RN27_ctaTrain to /data/Katz_Data/Stk11_Project/RN27/RN27_ctaTrain_200622_124440/RN27_ctaTrain_dataset.p

